Contacts of the strand formed by residues 221 - 225 (chain A) in PDB entry 1L1G
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR 221 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A LEU* 4.1 1.7 - - - +
174A CYS* 3.4 2.3 - - - -
175A ALA 3.0 34.9 + - - -
177A GLY 4.7 0.4 - - - +
182A SER* 3.7 12.8 - - - -
183A GLY* 2.9 35.5 + - - +
206A THR* 4.2 11.7 - - + -
208A PHE 3.9 9.6 - - - +
209A VAL* 4.0 13.1 - - + +
219A LYS 3.6 1.0 + - - -
220A PRO* 1.3 72.9 - - - +
222A VAL* 1.3 64.0 + - - +
223A PHE* 3.4 34.2 - - + -
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Residues in contact with VAL 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A TRP* 3.4 37.5 - - + +
168A VAL* 3.9 11.9 - - + -
172A MET* 3.7 28.9 - - + -
173A VAL 3.6 4.3 - - - +
174A CYS* 4.3 4.5 - - - -
206A THR* 3.9 0.9 - - - -
207A SER* 2.8 28.5 + - - -
208A PHE* 2.8 58.8 + - + +
220A PRO 3.4 3.4 - - - +
221A THR* 1.3 75.8 - - - +
223A PHE* 1.3 59.4 + - - +
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Residues in contact with PHE 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A ILE* 3.8 15.9 - - + -
150A LEU* 4.2 3.6 - - + -
172A MET* 3.1 10.3 - - - +
173A VAL* 2.8 44.4 + - + +
175A ALA* 3.7 16.8 - - + -
192A LEU* 3.7 42.8 - - + -
204A GLY* 3.8 15.7 - - - -
205A VAL 3.2 7.9 - - - +
206A THR* 3.2 41.5 - - - -
207A SER* 4.0 3.4 - - - +
221A THR* 3.4 38.4 - - + -
222A VAL* 1.3 75.9 - - - +
224A THR* 1.3 61.6 + - - +
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Residues in contact with THR 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A GLY* 6.1 0.2 - - - -
92A TYR 5.2 1.1 - - - +
93A ASP* 2.8 44.1 + - - +
94A ILE* 4.1 11.9 - - + -
171A SER 4.0 4.5 - - - +
172A MET* 4.5 3.1 - - - +
204A GLY* 3.3 5.2 - - - -
205A VAL* 2.8 38.8 + - - -
207A SER* 4.0 4.2 - - - -
223A PHE* 1.3 72.1 - - - +
225A ARG* 1.3 58.0 + - - +
226A VAL* 3.2 6.6 + - - +
229A TYR* 3.3 39.5 - - + +
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Residues in contact with ARG 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A GLY* 4.2 3.0 - - - -
119A THR 4.1 0.8 + - - +
120A ILE* 3.4 28.4 - - - +
170A ASN* 2.9 42.4 + - - +
171A SER* 2.9 25.1 + - - +
172A MET 3.9 2.5 - - - -
173A VAL* 3.6 17.3 - - + -
203A HIS* 3.7 6.3 - - - +
223A PHE 3.4 1.8 + - - -
224A THR* 1.3 69.1 - - - +
226A VAL* 1.3 65.3 + - - +
227A SER* 2.9 40.1 + - - +
228A ALA* 2.9 29.3 + - - +
229A TYR* 3.1 14.9 - - - -
263A BR 3.3 33.1 - - - +
266A BR 3.9 17.3 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il